Taxonomy Advancement and Genome Size Change: Two Perspectives on RNA Virus Genetic Diversity

ABSTRACT One paradigm to explain the complexity of viral RNA populations is that the low fidelity of the RNA-dependent RNA polymerase (RdRp) drives high mutation rates and consequently genetic diversity. Like most RNA viruses, wild-type yellow fever virus (YFV) replication is error-prone due to the lack of proofreading by the virus-encoded RdRp. However, there is evidence that replication of the live attenuated YF vaccine virus 17D, derived from wild-type strain Asibi, is less error-prone than wild-type RNA viruses. Recent studies comparing the genetic diversity of wild-type Asibi and 17D vaccine virus found that wild-type Asibi has the typical heterogeneous population of an RNA virus, while there is limited intra- and interpopulation variability of 17D vaccine virus. Utilizing chimeric and mutant infectious clone-derived viruses, we show that high and low genetic diversity profiles of wild-type Asibi virus and vaccine virus 17D, respectively, are multigenic. Introduction of either structural (pre-membrane and envelope) genes or NS2B or NS4B substitutions into the Asibi and 17D backbone resulted in altered variant population, nucleotide diversity, and mutation frequency compared to the parental viruses. Additionally, changes in genetic diversity of the chimeric and mutant viruses correlated with the phenotype of multiplication kinetics in human alveolar A549 cells. Overall, the paradigm that only the error-prone RdRp controls genetic diversity needs to be expanded to address the role of other genes in genetic diversity, and we hypothesize that it is the replication complex as a whole and not the RdRp alone that controls genetic diversity. IMPORTANCE With the advent of advanced sequencing technology, studies of RNA viruses have shown that genetic diversity can contribute to both attenuation and virulence and the paradigm is that this is controlled by the error-prone RNA-dependent RNA polymerase (RdRp). Since wild-type yellow fever virus (YFV) strain Asibi has genetic diversity typical of a wild-type RNA virus, while 17D virus vaccine has limited diversity, it provides a unique opportunity to investigate RNA population theory in the context of a well-characterized live attenuated vaccine. Utilizing infectious clone-derived viruses, we show that genetic diversity of RNA viruses is complex and that multiple genes, including structural genes and NS2B and NS4B genes also contribute to genetic diversity. We suggest that the replication complex as a whole, rather than only RdRp, drives genetic diversity, at least for YFV.

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A Pre-Vaccination Baseline of SARS-CoV-2 Genetic Surveillance and Diversity in the United States

Viruses ◽

10.3390/v14010104 ◽

2022 ◽

Vol 14 (1) ◽

pp. 104

Author(s):

Adam A. Capoferri ◽

Wei Shao ◽

Jon Spindler ◽

John M. Coffin ◽

Jason W. Rausch ◽

...

Keyword(s):

United States ◽

Genetic Diversity ◽

Rna Virus ◽

Viral Evolution ◽

The United States ◽

Virus Spread ◽

Immune Pressure ◽

Viral Genetic Diversity ◽

Genetic Sampling ◽

The U.S

COVID-19 vaccines were first administered on 15 December 2020, marking an important transition point for the spread of SARS-CoV-2 in the United States (U.S.). Prior to this point in time, the virus spread to an almost completely immunologically naïve population, whereas subsequently, vaccine-induced immune pressure and prior infections might be expected to influence viral evolution. Accordingly, we conducted a study to characterize the spread of SARS-CoV-2 in the U.S. pre-vaccination, investigate the depth and uniformity of genetic surveillance during this period, and measure and otherwise characterize changing viral genetic diversity, including by comparison with more recently emergent variants of concern (VOCs). In 2020, SARS-CoV-2 spread across the U.S. in three phases distinguishable by peaks in the numbers of infections and shifting geographical distributions. Virus was genetically sampled during this period at an overall rate of ~1.2%, though there was a substantial mismatch between case rates and genetic sampling nationwide. Viral genetic diversity tripled over this period but remained low in comparison to other widespread RNA virus pathogens, and although 54 amino acid changes were detected at frequencies exceeding 5%, linkage among them was not observed. Based on our collective observations, our analysis supports a targeted strategy for worldwide genetic surveillance as perhaps the most sensitive and efficient means of detecting new VOCs.

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Genetic diversity and genome size variability in Linum austriacum (Lineaceae) populations

Biochemical Systematics and Ecology ◽

10.1016/j.bse.2014.07.014 ◽

2014 ◽

Vol 57 ◽

pp. 20-26 ◽

Cited By ~ 17

Author(s):

Masoud Sheidai ◽

Fatima Afshar ◽

Maryam Keshavarzi ◽

Seyed-Mehdi Talebi ◽

Zahra Noormohammadi ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Size ◽

Size Variability

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New insights into the genetic diversity of Leishmania RNA Virus 1 and its species-specific relationship with Leishmania parasites

PLoS ONE ◽

10.1371/journal.pone.0198727 ◽

2018 ◽

Vol 13 (6) ◽

pp. e0198727 ◽

Cited By ~ 11

Author(s):

Lilian Motta Cantanhêde ◽

Flavia Gonçalves Fernandes ◽

Gabriel Eduardo Melim Ferreira ◽

Renato Porrozzi ◽

Ricardo de Godoi Mattos Ferreira ◽

...

Keyword(s):

Genetic Diversity ◽

Rna Virus ◽

Specific Relationship ◽

Species Specific ◽

Leishmania Parasites

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Genome Size: A Novel Predictor of Nut Weight and Nut Size of Walnut Trees

HortScience ◽

10.21273/hortsci12725-17 ◽

2018 ◽

Vol 53 (3) ◽

pp. 275-282 ◽

Cited By ~ 5

Author(s):

Saadat Sarikhani Khorami ◽

Kazem Arzani ◽

Ghasem Karimzadeh ◽

Abdolali Shojaeiyan ◽

Wilco Ligterink

Keyword(s):

Genetic Diversity ◽

Genome Size ◽

Plant Genetic Resources ◽

Kernel Weight ◽

High Yield ◽

Phenotypic Analysis ◽

High Genetic Diversity ◽

Breeding Programs ◽

Superior Genotypes ◽

Southwest Of Iran

Plant genetic diversity is the fundamental of plant-breeding programs to improve desirable characteristics. Hence, evaluation of genetic diversity is the first step in fruit-breeding programs. Accordingly, the current study was carried out to evaluate 25 superior walnut genotypes in respect of phenotypic and cytological characteristics. For this purpose, 560 walnut genotypes in southwest of Iran were evaluated based on UPOV and International Plant Genetic Resources Institute (IPGRI) descriptor. After a 2-year primary evaluation, 25 superior genotypes were selected for future phenotypic and genome size assessment. Flow cytometry was used to estimate genome size of the selected superior genotypes. A high genetic diversity was found in walnut population collected from the southwest of Iran. The selected superior genotypes had high yield, lateral bearing, thin-shell thickness (0.90–1.64 mm), high nut (12.54–19.80 g) and kernel (7.02–9.91 g) weight with light (L) to extra light (EL) kernel color which easily can be removed from the shell. Also, FaBaCh2 genotype turned out to be protogynous being important as a pollinizer cultivar. In addition to extensive phenotypic analysis, genome size was determined. The studied genotypes were diploid (2n = 2x = 32) and varied in genome size from 1.29 (FaBaAv2) to 1.40 pg (FaBaNs12). Correlation analysis showed that lateral bearing, budbreak date, nut size, and weight were the main variables contributing to walnut production. A linear relationship was found between genome size and nut weight (r = 0.527**), kernel weight (r = 0.551**), and nut size index (NSI) (r = 0.487**). Therefore, genome size can be considered as a strong and valuable tool to predict nut and kernel weight and nut size.

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Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses

Plant Disease ◽

10.1094/pdis-11-21-2409-re ◽

2022 ◽

Author(s):

Rochelle de Bruyn ◽

Rachelle Bester ◽

Glynnis Cook ◽

Chanel Steyn ◽

Johannes Hendrik Jacobus Breytenbach ◽

...

Keyword(s):

South Africa ◽

Genetic Diversity ◽

Real Time ◽

South African ◽

High Throughput Sequencing ◽

Rna Virus ◽

Citrus Paradisi ◽

Virus Elimination ◽

Shoot Tip Grafting ◽

Citrus Production

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus, was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit (Citrus paradisi Macf.), sweet orange (C. sinensis (L.) Osb.) and clementine (C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in ‘Delta’ Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the ‘Delta’ Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.

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